[Numpy-discussion] finding close together points.

Christopher Barker Chris.Barker at noaa.gov
Tue Nov 10 19:07:32 EST 2009

Hi all,

I have a bunch of points in 2-d space, and I need to find out which 
pairs of points are within a certain distance of one-another (regular 
old Euclidean norm).

scipy.spatial.KDTree.query_ball_tree() seems like it's built for this.

However, I'm a bit confused. The first argument is a kdtree, but I'm 
calling it as a method of a kdtree -- I want to know which points in the 
tree I already have are closer that some r from each-other.

If I call it as:

tree.query_ball_tree(tree, r)

I get a big list, that has all the points in it (some of them paired up 
with close neighbors.) It appears I'm getting the distances between all 
the points in the tree and itself, as though they were different trees.

This is slow, takes a bunch of memory, and I then have to parse out the 
list to find the ones that are paired up.

Is there a way to get just the close ones from the single tree?



Christopher Barker, Ph.D.

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Chris.Barker at noaa.gov

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